Chapter 4Distance–Based Methods of Phylogenetics
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第一部分听力(共两节，满分30分)第一节(共5小题；每小题1.5分，满分7.5分)听下面5段对话。
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1. Whose birthday is it today?A. Cassie’s.B. John’s.C. Ashley’s.2. What does the man think of Allan’s paintings?A. Funny.B. Terrible.C. So- so.3. What does the woman mean?A. David often eats his words.B. Her party was a success.C. Dr. Andrew put off his lecture.4. How do the speakers sound?A. Fine.B. Relaxed.C. Worried.5. What happened to Josh’s sister yesterday?A. She served the wrong dish.B. She got lost with her brother.C. She failed to behave herself in public.第二节(共15小题；每小题1.5分，满分22.5分)听下面5段对话或独白。
xaui_xgmii
– 4 Byte-wide lanes parallel interface with 1 control bit per lane • 156.25 Mbps, DDR signalling, source centred (3” max. distance) – 156.25 MHz clock (one TX, one RX) – 312.5 Mbps on each data/control line
10GE Interfaces – XAUI, XGMII, XSBI 7
XGMII – PHY/MAC Interface
10GE Interfaces – XAUI, XGMII, XSBI 8
10 GbE Interfaces - XSBI
• • • •
XSBI (10G Sixteen-Bit I/F) Based on OIF SFI-4.1 interface 644.53 Mbps, LVDS 34 pins: Tx/Rx (16 data (differential signals), 1 clock)
– Enables pluggable optical transceivers – Enables lower IC costs (pins = cost) – Longer trace lengths enable higher
density ICs (e.g., multiple MACs) and greater flexibility in board layout
XAUI - Interface Extender Between MAC & PCS
10GE Interfaces – XAUI, XGMII, XSBI 11
10GE Interfaces – XAUI, XGMII, XSBI 7
XGMII – PHY/MAC Interface
10GE Interfaces – XAUI, XGMII, XSBI 8
10 GbE Interfaces - XSBI
• • • •
XSBI (10G Sixteen-Bit I/F) Based on OIF SFI-4.1 interface 644.53 Mbps, LVDS 34 pins: Tx/Rx (16 data (differential signals), 1 clock)
– Enables pluggable optical transceivers – Enables lower IC costs (pins = cost) – Longer trace lengths enable higher
density ICs (e.g., multiple MACs) and greater flexibility in board layout
XAUI - Interface Extender Between MAC & PCS
10GE Interfaces – XAUI, XGMII, XSBI 11
gbether
The Ohio State University
Raj Jain 9-13
850 nm vs 1300 nm lasers
q
q
850 nm used in 10Base-F m Cannot go full distance with 62.5-µm fiber m 500 m with 50-µm fiber m 250 m with 62.5-µm fiber 1300 nm used in FDDI but more expensive m Higher eye safety limits m Better Reliability m Start with 550 m on 62.5-µm fiber m Could be improved to 2 km on 62.5-µm fiber ⇒ Needed for campus backbone
Raj Jain 9-2
The Ohio State University
Distance-B/W Principle
q q
q q
Efficiency = Max throughput/Media bandwidth Efficiency is a decreasing function of α α = Propagation delay /Transmission time = (Distance/Speed of light)/(Transmission size/Bits/sec) = Distance×Bits/sec/(Speed of light)(Transmission size) Bit rate-distance-transmission size tradeoff. 100 Mb/s ⇒ Change distance or frame size
分子进化树构建方法
MP法建树流程
Sequence1 Sequence2 Sequence3
Sequence4
Position 1
Position 1 2 3 T G C T A C A G G A A G
If 1 and 2 are grouped a total of four changes are needed.
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genetic change
系统发生树术语
Rooted tree vs. Unrooted tree
无 A 有 根 根 树 B 树 two major ways to root trees:
A
10 3 2 5
C D
By midpoint or distance
d (A,D) = 10 + 3 + 5 = 18 Midpoint = 18 / 2 = 9
Distance Uses only pairwise distances Minimizes distance between nearest neighbors Very fast Easily trapped in local optima Good for generating tentative tree, or choosing among multiple trees Maximum parsimony Uses only shared derived characters Minimizes total distance Maximum likelihood Uses all data Maximizes tree likelihood given specific parameter values Very slow Highly dependent on assumed evolution model Good for very small data sets and for testing trees built using other methods
物联网时代的短距离无线通信技术
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For Singlemode: LE only
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V2.1 + EDR
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•LE up to 260kbps •Including classic, LE and HS
物联网时代的 短距离无线通信技术
它用上无 线啦！
© Keysight Technologies 2015
物联网的基本构成
• 传感器 • 识别与传输 • 通信网络 • 后端应用
系统发育树构建
系统发育进化树示例 Figtree (树形显示软件）
系统发育分析是研究物种进化和系统分类的一种方法，研究对象为携带遗传信息的生物大分子序列，采用特定的数理统计算法来计算
生物间的生物系统发生的关系。
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系统发育树构建分析步骤
找到建树目的基因（基因组） 进行多序列比对 选择建树方法 建立进化树 进化树评估
• 系统进化树的主要构成： 结点（node)：每个结点表示一个分类单元（属、种群）。 进化分枝(Clade)： 是指由同一生物进化而来的单一系统群。 实体抽象为节点，实体间的进化关系抽象为连接
• 研究对象： 包括基因序列，基因组的排列方式，二级结构，编码的蛋白序列 及高级结构等
分子系统发育的核心是——构建系统发育进化树
• 名 称： Uncultured bacterium clone YU201H10 • 序列号： FJ694683 /FJ694514 • 文 献： TITLE Circumpolar synchrony in big river
bacterioplankton • 序列长度：353 • 相 似 比： 99% • 核酸序列 • 分类地位
打开软件clustalx
• CLUSTALX－是CLUSTAL多重序列比对程序的 Windows版本。Clustal X为进行多重序列和轮廓比 对和分析结果提供一个整体的环境。 序列将显示屏幕的窗口中。采用多色彩的模式可 以在比对中加亮保守区的特征。窗口上面的下拉 菜单可让你选择传统多重比对和轮廓比对需要的 所有选项。
进化支
猩 猩
系分M异i统子n根i的m发 系u：育统m的进发e所v化育数ol树的u有字ti（核on分心P(尺Mh是Ey类l—度)o最g—的e小。n构e进共建ti化c系t方r同e统e法)发祖育先进化。树
英汉翻译9翻译难点声色词
Splash plump thud 重物落下声 咕咚 Crash clank 东西倾倒声 哗啦 Rustle, whistle whir whish 风声 Murmur babble purl 泉水溪水流动声 潺潺 Creak crack snap 物体受压声 咯嚓 Bable gurgle 液体涌出或喝水声 咕咚 Flop thump splash pit-a-pat 重物落地或落水声 扑通 Titter, snigger, fizz 笑声或水气挤出的声音
A bull bellows (lows). 公牛哞哞叫。 A calf bleats. 小牛哞哞叫。 A cat miaows ( miaus, mews, purrs). 猫咪咪叫。 A chick cheeps (pips, peeps). 小鸡唧唧叫。
4.2 Translation of Color Words
色彩与人类的生活息息相关，是人类认识世界的一个重要领 域。色彩不仅具有物理属性，还有着丰富的文化内涵和延伸 意义，因此是语言、文化及翻译研究中的一个重要课题。
世界各民族语言表达颜色的词语多寡不一，分类各异。 英语和汉语对基本颜色词的分类差别不大。汉语中有赤、橙、 黄、绿、青、蓝、紫，英语中有red（红）， white（白）， black（黑），green（绿），yellow（黄），blue（蓝）， purple（紫），gray（灰），brown（棕）。这些基本颜色 之间有相同的方面，也有不同的区别。另外，受地理环境、 民情风俗、思维方式、宗教信仰、民族心理等因素的影响， 各种颜色对于不同民族的人而言，在视觉和心理上所引发的 联想和象征意义也不尽相同，翻译时应该特别注意其中的差 异。下面我们简要列举几个主要颜色词在英语和汉语中的对 比。
phylip使用说明
Phylogeny ProgramsUPGMA (PHYLIP: neighbour)除权配对法Neighbour Joining (PHYLIP: neighbour)临近距离法Fitch-Margoliash (PHYLIP: fitch)Maximum Parsimony 最大简约性法DNA sequences (PHYLIP: dnapars)Protein sequences (PHYLIP: protpars)Maximum Likelihood 最大可能性法DNA sequences (PHYLIP: fastDNAML, Molphy: nucML)Protein sequences (Molphy: protML)对于一个完整的进化树分析需要以下几个步骤：⑴要对所分析的多序列目标进行排列（T o align sequences）。
⑵要构建一个进化树（T o reconstrut phyligenetic tree）。
构建进化树的算法主要分为两类：独立元素法（discrete character methods）和距离依靠法（distance methods）。
独立元素法：指进化树的拓扑形状是由序列上的每个碱基/氨基酸的状态决定的（例如：一个序列上可能包含很多的酶切位点，而每个酶切位点的存在与否是由几个碱基的状态决定的，也就是说一个序列碱基的状态决定着它的酶切位点状态，当多个序列进行进化树分析时，进化树的拓扑形状也就由这些碱基的状态决定了）。
独立元素法包括最大简约性法（Maximum Parsimony methods）和最大可能性法（Maximum Likelihood methods）；距离依靠法是指进化树的拓扑形状由两两序列的进化距离决定的。
进化树枝条的长度代表着进化距离。
距离依靠法包括除权配对法（UPGMAM）和邻位相连法（Neighbor-joining）。
⑶对进化树进行评估。
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We focus on cluster analysis in this chapter.
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比較解剖學
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蟒蛇與人
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Linnaeus
林奈
十八世紀博物學家 帶領未受訓練的學生到世界各地蒐集標本, 遠征過 程中有三分之一的學生死亡. 創立「二名法」(binomial system of nomenclature)
屬名(genus)＋種名(species)
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4.2 Advantages of Molecular Phylogenies
fundamental
evolution is defined as genetic changes molecular clock hypothesis (Chap. 3)
collected data (I, II, III, IV, V) inferred ancestors (A, B, C, D)
internal nodes
Newick format
(((I, II), (III, IV)), V)
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4.3.2 Rooted and Unrooted Trees
many organisms do not have easily studied phenotypic features
bacteria (細菌) bacteria, worms, mammals few characteristics in common!
comparing distantly related organisms
Chapter 4 Distance–Based Methods of Phylogenetics
暨南大學資訊工程學系 黃光璿 (HUANG, Guan-Shieng) 2004/03/29
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Motivation
Evolution events on genomes:
substitutions insertions deletions rearrangements
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4.3 Phylogenetic Trees
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4.3.1 Terminology of Tree Reconstruction
phylogenetic tree, or dendrogram
nodes: taxonomical units branches terminal nodes
Four-point condition dAB+dCD<dAC+dBD dAB+dCD<dAD+dBC holds if the tree is additive.
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Given any four points, say A, B, C, D, we have dAB+dCD dAC+dBD dAD+dBC. The smallest indicates how to pair up.
UPGMA (Unweighted-Pair-Group Method with Arithmetic mean) Transformed Distance Method Neighbor’s Relation Method Neighbor-Joining Method
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4.4.3 Neighbor’s Relation Method
character data distance data pheneticist: prefers distance based methods cladist: prefer character based methods
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4.4 Distance Matrix Methods
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4.4.4 Neighbor-Joining Methods
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(7.4)
where
L:the set of all leaves
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Theorem
If a matrix is additive, then its phylogenetic tree (unrooted, binary) can be reconstructed correctly and uniquely by the Neighbor-Joining Method.
In early days, taxonomists inferred genotypes from phenotypes.
phenotypes(表現型): how organisms looks genotypes: the genes that gave rise to their physical appearance
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S. Sattath & A. Tversky, 1977 For any four points, say A, B, C, D, compute dAB+dCD dAC+dBD dAD+dBC. The smallest should be paired, and wins a score 1 for each pair. After trying all possible quadruples, the pair wins the highest scores is grouped.
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Example
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The length of the branches can be determined by the outgroup method.
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Theorem
If a matrix is additive, then its phylogenetic tree (unrooted, binary) can be reconstructed correctly and uniquely by the Neighbor’s Relation hen
behavior (行為) ultrastructural (超顯微結構) biochemical characteristics
were studied.
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傳統研究方法有以下問題無法解決
convergent evolution
眼睛：humans, flies, mollusks (軟體動物)
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參考資料及圖片出處
1.
2.
3.
Fundamental Concepts of Bioinformatics Dan E. Krane and Michael L. Raymer, Benjamin/Cummings, 2003. Biological Sequence Analysis – Probabilistic models of proteins and nucleic acids R. Durbin, S. Eddy, A. Krogh, G. Mitchison, Cambridge University Press, 1998. Biology, by Sylvia S. Mader, 8th edition, McGraw-Hill, 2003.
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4.3.4 Character and Distance Data
characters (特質)
DNA sequences, protein sequences, color, behavior, response time, ……
distance
overall, pairwise difference
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